Well that's the problem, at least as far as I'm concerned. I concede I could be completely full of crap on this but it's just my gut feeling, and it's somewhat/possibly confirmed by the issues people have with the M&P9 that aren't seen on the 40 (I've heard of ejection issues). But the gun was designed around the 40S&W round and they later released a 9mm version by making the barrel thicker. Timing an automatic for one caliber is hard enough, so trying to make it generic for multiple seems like an idea destined to fail.
My main concerns would be the extractor and the recoil spring tension. But for the recoil spring you can get uncaptured rods and spring sets from Wolff, and try different things until you get that wonderfully consistent 100 foot ejection pattern the M&P is known for. From the anecdotal evidence I heard, the M&P9 becomes much more accurate with 147 gr ammo, which seems to support the idea that it's a gun designed for 40 cal bullets but with a thicker barrel fitted.